src/jalview/bin/Jalview.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.bin;
  22
  23 import jalview.ext.so.SequenceOntology;
  24 import jalview.gui.AlignFrame;
  25 import jalview.gui.Desktop;
  26 import jalview.gui.PromptUserConfig;
  27 import jalview.io.AppletFormatAdapter;
  28 import jalview.io.BioJsHTMLOutput;
  29 import jalview.io.DataSourceType;
  30 import jalview.io.FileFormat;
  31 import jalview.io.FileFormatException;
  32 import jalview.io.FileFormatI;
  33 import jalview.io.FileLoader;
  34 import jalview.io.HtmlSvgOutput;
  35 import jalview.io.IdentifyFile;
  36 import jalview.io.NewickFile;
  37 import jalview.io.gff.SequenceOntologyFactory;
  38 import jalview.schemes.ColourSchemeI;
  39 import jalview.schemes.ColourSchemeProperty;
  40 import jalview.util.MessageManager;
  41 import jalview.util.Platform;
  42 import jalview.ws.jws2.Jws2Discoverer;
  43
  44 import java.io.BufferedReader;
  45 import java.io.File;
  46 import java.io.FileOutputStream;
  47 import java.io.IOException;
  48 import java.io.InputStreamReader;
  49 import java.io.OutputStreamWriter;
  50 import java.io.PrintWriter;
  51 import java.net.MalformedURLException;
  52 import java.net.URI;
  53 import java.net.URISyntaxException;
  54 import java.net.URL;
  55 import java.security.AllPermission;
  56 import java.security.CodeSource;
  57 import java.security.PermissionCollection;
  58 import java.security.Permissions;
  59 import java.security.Policy;
  60 import java.util.HashMap;
  61 import java.util.Map;
  62 import java.util.Vector;
  63
  64 import javax.swing.LookAndFeel;
  65 import javax.swing.UIManager;
  66
  67 import com.threerings.getdown.util.LaunchUtil;
  68
  69 import groovy.lang.Binding;
  70 import groovy.util.GroovyScriptEngine;
  71
  72 /**
  73  * Main class for Jalview Application <br>
  74  * <br>
  75  * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
  76  * jalview.bin.Jalview
  77  *
  78  * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
  79  * jalview.bin.Jalview jalview.bin.Jalview
  80  *
  81  * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
  82  * embellish '*' to e.g. '*.jar')
  83  *
  84  * @author $author$
  85  * @version $Revision$
  86  */
  87 public class Jalview
  88 {
  89         /*
  90          * singleton instance of this class
  91          */
  92         private static Jalview instance;
  93
  94         private Desktop desktop;
  95
  96         public static AlignFrame currentAlignFrame;
  97
  98         static {
  99                 // grab all the rights we can the JVM
 100                 Policy.setPolicy(new Policy() {
 101                         @Override
 102                         public PermissionCollection getPermissions(CodeSource codesource) {
 103                                 Permissions perms = new Permissions();
 104                                 perms.add(new AllPermission());
 105                                 return (perms);
 106                         }
 107
 108                         @Override
 109                         public void refresh() {
 110                         }
 111                 });
 112         }
 113
 114         /**
 115          * keep track of feature fetching tasks.
 116          *
 117          * @author JimP
 118          *
 119          */
 120         class FeatureFetcher {
 121                 /*
 122                  * TODO: generalise to track all jalview events to orchestrate batch processing
 123                  * events.
 124                  */
 125
 126                 private int queued = 0;
 127
 128                 private int running = 0;
 129
 130                 public FeatureFetcher() {
 131
 132                 }
 133
 134                 public void addFetcher(final AlignFrame af, final Vector<String> dasSources) {
 135                         final long id = System.currentTimeMillis();
 136                         queued++;
 137                         final FeatureFetcher us = this;
 138                         new Thread(new Runnable() {
 139
 140                                 @Override
 141                                 public void run() {
 142                                         synchronized (us) {
 143                                                 queued--;
 144                                                 running++;
 145                                         }
 146
 147                                         af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
 148                                         af.featureSettings_actionPerformed(null);
 149                                         af.setProgressBar(null, id);
 150                                         synchronized (us) {
 151                                                 running--;
 152                                         }
 153                                 }
 154                         }).start();
 155                 }
 156
 157                 public synchronized boolean allFinished() {
 158                         return queued == 0 && running == 0;
 159                 }
 160
 161         }
 162
 163         public static Jalview getInstance() {
 164                 return instance;
 165         }
 166
 167         /**
 168          * main class for Jalview application
 169          *
 170          * @param args open <em>filename</em>
 171          */
 172         public static void main(String[] args) {
 173                 instance = new Jalview();
 174                 instance.doMain(args);
 175         }
 176
 177         /**
 178          * @param args
 179          */
 180         void doMain(String[] args) {
 181                 System.setSecurityManager(null);
 182                 System.out.println("Java version: " + System.getProperty("java.version"));
 183                 System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " "
 184                                 + System.getProperty("os.version"));
 185                 // report Jalview version
 186                 Cache.loadBuildProperties(true);
 187
 188                 ArgsParser aparser = new ArgsParser(args);
 189                 boolean headless = false;
 190
 191                 if (aparser.contains("help") || aparser.contains("h")) {
 192                         showUsage();
 193                         System.exit(0);
 194                 }
 195                 if (aparser.contains("nodisplay") || aparser.contains("nogui") || aparser.contains("headless")) {
 196                         System.setProperty("java.awt.headless", "true");
 197                         headless = true;
 198                 }
 199                 String usrPropsFile = aparser.getValue("props");
 200                 Cache.loadProperties(usrPropsFile); // must do this before
 201                 if (usrPropsFile != null) {
 202                         System.out.println("CMD [-props " + usrPropsFile + "] executed successfully!");
 203                 }
 204
 205                 // anything else!
 206
 207                 final String jabawsUrl = aparser.getValue("jabaws");
 208                 if (jabawsUrl != null) {
 209                         try {
 210                                 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
 211                                 System.out.println("CMD [-jabaws " + jabawsUrl + "] executed successfully!");
 212                         } catch (MalformedURLException e) {
 213                                 System.err.println("Invalid jabaws parameter: " + jabawsUrl + " ignored");
 214                         }
 215                 }
 216
 217                 String defs = aparser.getValue("setprop");
 218                 while (defs != null) {
 219                         int p = defs.indexOf('=');
 220                         if (p == -1) {
 221                                 System.err.println("Ignoring invalid setprop argument : " + defs);
 222                         } else {
 223                                 System.out.println("Executing setprop argument: " + defs);
 224                                 // DISABLED FOR SECURITY REASONS
 225                                 // TODO: add a property to allow properties to be overriden by cli args
 226                                 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
 227                         }
 228                         defs = aparser.getValue("setprop");
 229                 }
 230                 if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) {
 231                         headless = true;
 232                 }
 233                 System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
 234                 try {
 235                         Cache.initLogger();
 236                 } catch (NoClassDefFoundError error) {
 237                         error.printStackTrace();
 238                         System.out.println("\nEssential logging libraries not found."
 239                                         + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
 240                         System.exit(0);
 241                 }
 242
 243                 desktop = null;
 244
 245                 try {
 246                         UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
 247                 } catch (Exception ex) {
 248                         System.err.println("Unexpected Look and Feel Exception");
 249                         ex.printStackTrace();
 250                 }
 251                 if (Platform.isAMac()) {
 252
 253                         LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel();
 254                         System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview");
 255                         System.setProperty("apple.laf.useScreenMenuBar", "true");
 256                         if (lookAndFeel != null) {
 257                                 try {
 258                                         UIManager.setLookAndFeel(lookAndFeel);
 259                                 } catch (Throwable e) {
 260                                         System.err.println("Failed to set QuaQua look and feel: " + e.toString());
 261                                 }
 262                         }
 263                         if (lookAndFeel == null || !(lookAndFeel.getClass().isAssignableFrom(UIManager.getLookAndFeel().getClass()))
 264                                         || !UIManager.getLookAndFeel().getClass().toString().toLowerCase().contains("quaqua")) {
 265                                 try {
 266                                         System.err.println(
 267                                                         "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
 268                                         UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
 269                                 } catch (Throwable e) {
 270                                         System.err.println("Failed to reset look and feel: " + e.toString());
 271                                 }
 272                         }
 273                 }
 274
 275                 /*
 276                  * configure 'full' SO model if preferences say to, else use the default (SO
 277                  * Lite)
 278                  */
 279                 if (Cache.getDefault("USE_FULL_SO", false)) {
 280                         SequenceOntologyFactory.setInstance(new SequenceOntology());
 281                 }
 282
 283                 if (!headless) {
 284                         desktop = new Desktop();
 285                         desktop.setInBatchMode(true); // indicate we are starting up
 286
 287                         try {
 288                                 JalviewTaskbar.setTaskbar(this);
 289                         } catch (Exception e) {
 290                                 System.out.println("Cannot set Taskbar");
 291                                 // e.printStackTrace();
 292                         } catch (Throwable t) {
 293                                 System.out.println("Cannot set Taskbar");
 294                                 // t.printStackTrace();
 295                         }
 296
 297                         desktop.setVisible(true);
 298                         desktop.startServiceDiscovery();
 299                         if (!aparser.contains("nousagestats")) {
 300                                 startUsageStats(desktop);
 301                         } else {
 302                                 System.err.println("CMD [-nousagestats] executed successfully!");
 303                         }
 304
 305                         if (!aparser.contains("noquestionnaire")) {
 306                                 String url = aparser.getValue("questionnaire");
 307                                 if (url != null) {
 308                                         // Start the desktop questionnaire prompter with the specified
 309                                         // questionnaire
 310                                         Cache.log.debug("Starting questionnaire url at " + url);
 311                                         desktop.checkForQuestionnaire(url);
 312                                         System.out.println("CMD questionnaire[-" + url + "] executed successfully!");
 313                                 } else {
 314                                         if (Cache.getProperty("NOQUESTIONNAIRES") == null) {
 315                                                 // Start the desktop questionnaire prompter with the specified
 316                                                 // questionnaire
 317                                                 // String defurl =
 318                                                 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
 319                                                 // //
 320                                                 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
 321                                                 Cache.log.debug("Starting questionnaire with default url: " + defurl);
 322                                                 desktop.checkForQuestionnaire(defurl);
 323                                         }
 324                                 }
 325                         } else {
 326                                 System.err.println("CMD [-noquestionnaire] executed successfully!");
 327                         }
 328
 329                         if (!aparser.contains("nonews")) {
 330                                 desktop.checkForNews();
 331                         }
 332
 333                         BioJsHTMLOutput.updateBioJS();
 334                 }
 335
 336                 // Move any new getdown-launcher-new.jar into place over old
 337                 // getdown-launcher.jar
 338                 String appdirString = System.getProperty("getdownappdir");
 339                 if (appdirString != null && appdirString.length() > 0) {
 340                         final File appdir = new File(appdirString);
 341                         new Thread() {
 342                                 @Override
 343                                 public void run() {
 344                                         LaunchUtil.upgradeGetdown(new File(appdir, "getdown-launcher-old.jar"),
 345                                                         new File(appdir, "getdown-launcher.jar"), new File(appdir, "getdown-launcher-new.jar"));
 346                                 }
 347                         }.start();
 348                 }
 349
 350                 String file = null, data = null;
 351                 FileFormatI format = null;
 352                 DataSourceType protocol = null;
 353                 FileLoader fileLoader = new FileLoader(!headless);
 354
 355                 String groovyscript = null; // script to execute after all loading is
 356                 // completed one way or another
 357                 // extract groovy argument and execute if necessary
 358                 groovyscript = aparser.getValue("groovy", true);
 359                 file = aparser.getValue("open", true);
 360
 361                 if (file == null && desktop == null) {
 362                         System.out.println("No files to open!");
 363                         System.exit(1);
 364                 }
 365                 String vamsasImport = aparser.getValue("vdoc");
 366                 String vamsasSession = aparser.getValue("vsess");
 367                 if (vamsasImport != null || vamsasSession != null) {
 368                         if (desktop == null || headless) {
 369                                 System.out.println("Headless vamsas sessions not yet supported. Sorry.");
 370                                 System.exit(1);
 371                         }
 372                         // if we have a file, start a new session and import it.
 373                         boolean inSession = false;
 374                         if (vamsasImport != null) {
 375                                 try {
 376                                         DataSourceType viprotocol = AppletFormatAdapter.checkProtocol(vamsasImport);
 377                                         if (viprotocol == DataSourceType.FILE) {
 378                                                 inSession = desktop.vamsasImport(new File(vamsasImport));
 379                                         } else if (viprotocol == DataSourceType.URL) {
 380                                                 inSession = desktop.vamsasImport(new URL(vamsasImport));
 381                                         }
 382
 383                                 } catch (Exception e) {
 384                                         System.err.println("Exeption when importing " + vamsasImport + " as a vamsas document.");
 385                                         e.printStackTrace();
 386                                 }
 387                                 if (!inSession) {
 388                                         System.err.println("Failed to import " + vamsasImport + " as a vamsas document.");
 389                                 } else {
 390                                         System.out.println("Imported Successfully into new session "
 391                                                         + desktop.getVamsasApplication().getCurrentSession());
 392                                 }
 393                         }
 394                         if (vamsasSession != null) {
 395                                 if (vamsasImport != null) {
 396                                         // close the newly imported session and import the Jalview specific
 397                                         // remnants into the new session later on.
 398                                         desktop.vamsasStop_actionPerformed(null);
 399                                 }
 400                                 // now join the new session
 401                                 try {
 402                                         if (desktop.joinVamsasSession(vamsasSession)) {
 403                                                 System.out.println("Successfully joined vamsas session " + vamsasSession);
 404                                         } else {
 405                                                 System.err.println("WARNING: Failed to join vamsas session " + vamsasSession);
 406                                         }
 407                                 } catch (Exception e) {
 408                                         System.err.println("ERROR: Failed to join vamsas session " + vamsasSession);
 409                                         e.printStackTrace();
 410                                 }
 411                                 if (vamsasImport != null) {
 412                                         // the Jalview specific remnants can now be imported into the new
 413                                         // session at the user's leisure.
 414                                         Cache.log.info("Skipping Push for import of data into existing vamsas session."); // TODO:
 415                                         // enable
 416                                         // this
 417                                         // when
 418                                         // debugged
 419                                         // desktop.getVamsasApplication().push_update();
 420                                 }
 421                         }
 422                 }
 423                 long progress = -1;
 424                 // Finally, deal with the remaining input data.
 425                 if (file != null) {
 426                         if (!headless) {
 427                                 desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
 428                                                 progress = System.currentTimeMillis());
 429                         }
 430                         System.out.println("CMD [-open " + file + "] executed successfully!");
 431
 432                         if (!file.startsWith("http://")) {
 433                                 if (!(new File(file)).exists()) {
 434                                         System.out.println("Can't find " + file);
 435                                         if (headless) {
 436                                                 System.exit(1);
 437                                         }
 438                                 }
 439                         }
 440
 441                         protocol = AppletFormatAdapter.checkProtocol(file);
 442
 443                         try {
 444                                 format = new IdentifyFile().identify(file, protocol);
 445                         } catch (FileFormatException e1) {
 446                                 // TODO ?
 447                         }
 448
 449                         AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 450                         if (af == null) {
 451                                 System.out.println("error");
 452                         } else {
 453                                 setCurrentAlignFrame(af);
 454                                 data = aparser.getValue("colour", true);
 455                                 if (data != null) {
 456                                         data.replaceAll("%20", " ");
 457
 458                                         ColourSchemeI cs = ColourSchemeProperty.getColourScheme(af.getViewport(),
 459                                                         af.getViewport().getAlignment(), data);
 460
 461                                         if (cs != null) {
 462                                                 System.out.println("CMD [-color " + data + "] executed successfully!");
 463                                         }
 464                                         af.changeColour(cs);
 465                                 }
 466
 467                                 // Must maintain ability to use the groups flag
 468                                 data = aparser.getValue("groups", true);
 469                                 if (data != null) {
 470                                         af.parseFeaturesFile(data, AppletFormatAdapter.checkProtocol(data));
 471                                         // System.out.println("Added " + data);
 472                                         System.out.println("CMD groups[-" + data + "]  executed successfully!");
 473                                 }
 474                                 data = aparser.getValue("features", true);
 475                                 if (data != null) {
 476                                         af.parseFeaturesFile(data, AppletFormatAdapter.checkProtocol(data));
 477                                         // System.out.println("Added " + data);
 478                                         System.out.println("CMD [-features " + data + "]  executed successfully!");
 479                                 }
 480
 481                                 data = aparser.getValue("annotations", true);
 482                                 if (data != null) {
 483                                         af.loadJalviewDataFile(data, null, null, null);
 484                                         // System.out.println("Added " + data);
 485                                         System.out.println("CMD [-annotations " + data + "] executed successfully!");
 486                                 }
 487                                 // set or clear the sortbytree flag.
 488                                 if (aparser.contains("sortbytree")) {
 489                                         af.getViewport().setSortByTree(true);
 490                                         if (af.getViewport().getSortByTree()) {
 491                                                 System.out.println("CMD [-sortbytree] executed successfully!");
 492                                         }
 493                                 }
 494                                 if (aparser.contains("no-annotation")) {
 495                                         af.getViewport().setShowAnnotation(false);
 496                                         if (!af.getViewport().isShowAnnotation()) {
 497                                                 System.out.println("CMD no-annotation executed successfully!");
 498                                         }
 499                                 }
 500                                 if (aparser.contains("nosortbytree")) {
 501                                         af.getViewport().setSortByTree(false);
 502                                         if (!af.getViewport().getSortByTree()) {
 503                                                 System.out.println("CMD [-nosortbytree] executed successfully!");
 504                                         }
 505                                 }
 506                                 data = aparser.getValue("tree", true);
 507                                 if (data != null) {
 508                                         try {
 509                                                 System.out.println("CMD [-tree " + data + "] executed successfully!");
 510                                                 NewickFile nf = new NewickFile(data, AppletFormatAdapter.checkProtocol(data));
 511                                                 af.getViewport().setCurrentTree(af.showNewickTree(nf, data).getTree());
 512                                         } catch (IOException ex) {
 513                                                 System.err.println("Couldn't add tree " + data);
 514                                                 ex.printStackTrace(System.err);
 515                                         }
 516                                 }
 517                                 // TODO - load PDB structure(s) to alignment JAL-629
 518                                 // (associate with identical sequence in alignment, or a specified
 519                                 // sequence)
 520                                 if (groovyscript != null) {
 521                                         // Execute the groovy script after we've done all the rendering stuff
 522                                         // and before any images or figures are generated.
 523                                         System.out.println("Executing script " + groovyscript);
 524                                         executeGroovyScript(groovyscript, af);
 525                                         System.out.println("CMD groovy[" + groovyscript + "] executed successfully!");
 526                                         groovyscript = null;
 527                                 }
 528                                 String imageName = "unnamed.png";
 529                                 while (aparser.getSize() > 1) {
 530                                         String outputFormat = aparser.nextValue();
 531                                         file = aparser.nextValue();
 532
 533                                         if (outputFormat.equalsIgnoreCase("png")) {
 534                                                 af.createPNG(new File(file));
 535                                                 imageName = (new File(file)).getName();
 536                                                 System.out.println("Creating PNG image: " + file);
 537                                                 continue;
 538                                         } else if (outputFormat.equalsIgnoreCase("svg")) {
 539                                                 File imageFile = new File(file);
 540                                                 imageName = imageFile.getName();
 541                                                 af.createSVG(imageFile);
 542                                                 System.out.println("Creating SVG image: " + file);
 543                                                 continue;
 544                                         } else if (outputFormat.equalsIgnoreCase("html")) {
 545                                                 File imageFile = new File(file);
 546                                                 imageName = imageFile.getName();
 547                                                 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
 548                                                 htmlSVG.exportHTML(file);
 549
 550                                                 System.out.println("Creating HTML image: " + file);
 551                                                 continue;
 552                                         } else if (outputFormat.equalsIgnoreCase("biojsmsa")) {
 553                                                 if (file == null) {
 554                                                         System.err.println("The output html file must not be null");
 555                                                         return;
 556                                                 }
 557                                                 try {
 558                                                         BioJsHTMLOutput.refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
 559                                                 } catch (URISyntaxException e) {
 560                                                         e.printStackTrace();
 561                                                 }
 562                                                 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
 563                                                 bjs.exportHTML(file);
 564                                                 System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
 565                                                 continue;
 566                                         } else if (outputFormat.equalsIgnoreCase("imgMap")) {
 567                                                 af.createImageMap(new File(file), imageName);
 568                                                 System.out.println("Creating image map: " + file);
 569                                                 continue;
 570                                         } else if (outputFormat.equalsIgnoreCase("eps")) {
 571                                                 File outputFile = new File(file);
 572                                                 System.out.println("Creating EPS file: " + outputFile.getAbsolutePath());
 573                                                 af.createEPS(outputFile);
 574                                                 continue;
 575                                         }
 576
 577                                         if (af.saveAlignment(file, format)) {
 578                                                 System.out.println("Written alignment in " + format + " format to " + file);
 579                                         } else {
 580                                                 System.out.println("Error writing file " + file + " in " + format + " format!!");
 581                                         }
 582
 583                                 }
 584
 585                                 while (aparser.getSize() > 0) {
 586                                         System.out.println("Unknown arg: " + aparser.nextValue());
 587                                 }
 588                         }
 589                 }
 590                 AlignFrame startUpAlframe = null;
 591                 // We'll only open the default file if the desktop is visible.
 592                 // And the user
 593                 // ////////////////////
 594
 595                 if (!headless && file == null && vamsasImport == null
 596                                 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) {
 597                         file = jalview.bin.Cache.getDefault("STARTUP_FILE",
 598                                         jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 599                                                         + "/examples/exampleFile_2_7.jar");
 600                         if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")) {
 601                                 // hardwire upgrade of the startup file
 602                                 file.replace("_2_3.jar", "_2_7.jar");
 603                                 // and remove the stale setting
 604                                 jalview.bin.Cache.removeProperty("STARTUP_FILE");
 605                         }
 606
 607                         protocol = DataSourceType.FILE;
 608
 609                         if (file.indexOf("http:") > -1) {
 610                                 protocol = DataSourceType.URL;
 611                         }
 612
 613                         if (file.endsWith(".jar")) {
 614                                 format = FileFormat.Jalview;
 615                         } else {
 616                                 try {
 617                                         format = new IdentifyFile().identify(file, protocol);
 618                                 } catch (FileFormatException e) {
 619                                         // TODO what?
 620                                 }
 621                         }
 622
 623                         startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
 624                         // extract groovy arguments before anything else.
 625                 }
 626
 627                 // Once all other stuff is done, execute any groovy scripts (in order)
 628                 if (groovyscript != null) {
 629                         if (Cache.groovyJarsPresent()) {
 630                                 System.out.println("Executing script " + groovyscript);
 631                                 executeGroovyScript(groovyscript, startUpAlframe);
 632                         } else {
 633                                 System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
 634                                                 + groovyscript);
 635                         }
 636                 }
 637                 // and finally, turn off batch mode indicator - if the desktop still exists
 638                 if (desktop != null) {
 639                         if (progress != -1) {
 640                                 desktop.setProgressBar(null, progress);
 641                         }
 642                         desktop.setInBatchMode(false);
 643                 }
 644         }
 645
 646         private static void showUsage() {
 647                 System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
 648                                 + "-nodisplay\tRun Jalview without User Interface.\n"
 649                                 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
 650                                 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
 651                                 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
 652                                 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
 653                                 + "-features FILE\tUse the given file to mark features on the alignment.\n"
 654                                 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
 655                                 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
 656                                 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
 657                                 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
 658                                 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
 659                                 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
 660                                 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
 661                                 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
 662                                 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
 663                                 + "-png FILE\tCreate PNG image FILE from alignment.\n"
 664                                 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
 665                                 + "-html FILE\tCreate HTML file from alignment.\n"
 666                                 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
 667                                 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
 668                                 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
 669                                 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
 670                                 + "-noquestionnaire\tTurn off questionnaire check.\n" + "-nonews\tTurn off check for Jalview news.\n"
 671                                 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
 672                                 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
 673                                 // +
 674                                 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
 675                                 // after all other properties files have been read\n\t
 676                                 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
 677                                 // passed in correctly)"
 678                                 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
 679                                 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
 680                                 // +
 681                                 // "-vdoc vamsas-document\tImport vamsas document into new
 682                                 // session or join existing session with same URN\n"
 683                                 // + "-vses vamsas-session\tJoin session with given URN\n"
 684                                 + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
 685                                 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
 686         }
 687
 688         private static void startUsageStats(final Desktop desktop) {
 689                 /**
 690                  * start a User Config prompt asking if we can log usage statistics.
 691                  */
 692                 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, "USAGESTATS", "Jalview Usage Statistics",
 693                                 "Do you want to help make Jalview better by enabling "
 694                                                 + "the collection of usage statistics with Google Analytics ?"
 695                                                 + "\n\n(you can enable or disable usage tracking in the preferences)",
 696                                 new Runnable() {
 697                                         @Override
 698                                         public void run() {
 699                                                 Cache.log.debug("Initialising googletracker for usage stats.");
 700                                                 Cache.initGoogleTracker();
 701                                                 Cache.log.debug("Tracking enabled.");
 702                                         }
 703                                 }, new Runnable() {
 704                                         @Override
 705                                         public void run() {
 706                                                 Cache.log.debug("Not enabling Google Tracking.");
 707                                         }
 708                                 }, null, true);
 709                 desktop.addDialogThread(prompter);
 710         }
 711
 712         /**
 713          * Locate the given string as a file and pass it to the groovy interpreter.
 714          *
 715          * @param groovyscript   the script to execute
 716          * @param jalviewContext the Jalview Desktop object passed in to the groovy
 717          *                       binding as the 'Jalview' object.
 718          */
 719         private void executeGroovyScript(String groovyscript, AlignFrame af) {
 720                 /**
 721                  * for scripts contained in files
 722                  */
 723                 File tfile = null;
 724                 /**
 725                  * script's URI
 726                  */
 727                 URL sfile = null;
 728                 if (groovyscript.trim().equals("STDIN")) {
 729                         // read from stdin into a tempfile and execute it
 730                         try {
 731                                 tfile = File.createTempFile("jalview", "groovy");
 732                                 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(tfile)));
 733                                 BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
 734                                 String line = null;
 735                                 while ((line = br.readLine()) != null) {
 736                                         outfile.write(line + "\n");
 737                                 }
 738                                 br.close();
 739                                 outfile.flush();
 740                                 outfile.close();
 741
 742                         } catch (Exception ex) {
 743                                 System.err.println("Failed to read from STDIN into tempfile "
 744                                                 + ((tfile == null) ? "(tempfile wasn't created)" : tfile.toString()));
 745                                 ex.printStackTrace();
 746                                 return;
 747                         }
 748                         try {
 749                                 sfile = tfile.toURI().toURL();
 750                         } catch (Exception x) {
 751                                 System.err.println(
 752                                                 "Unexpected Malformed URL Exception for temporary file created from STDIN: " + tfile.toURI());
 753                                 x.printStackTrace();
 754                                 return;
 755                         }
 756                 } else {
 757                         try {
 758                                 sfile = new URI(groovyscript).toURL();
 759                         } catch (Exception x) {
 760                                 tfile = new File(groovyscript);
 761                                 if (!tfile.exists()) {
 762                                         System.err.println("File '" + groovyscript + "' does not exist.");
 763                                         return;
 764                                 }
 765                                 if (!tfile.canRead()) {
 766                                         System.err.println("File '" + groovyscript + "' cannot be read.");
 767                                         return;
 768                                 }
 769                                 if (tfile.length() < 1) {
 770                                         System.err.println("File '" + groovyscript + "' is empty.");
 771                                         return;
 772                                 }
 773                                 try {
 774                                         sfile = tfile.getAbsoluteFile().toURI().toURL();
 775                                 } catch (Exception ex) {
 776                                         System.err.println("Failed to create a file URL for " + tfile.getAbsoluteFile());
 777                                         return;
 778                                 }
 779                         }
 780                 }
 781                 try {
 782                         Map<String, java.lang.Object> vbinding = new HashMap<>();
 783                         vbinding.put("Jalview", this);
 784                         if (af != null) {
 785                                 vbinding.put("currentAlFrame", af);
 786                         }
 787                         Binding gbinding = new Binding(vbinding);
 788                         GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
 789                         gse.run(sfile.toString(), gbinding);
 790                         if ("STDIN".equals(groovyscript)) {
 791                                 // delete temp file that we made -
 792                                 // only if it was successfully executed
 793                                 tfile.delete();
 794                         }
 795                 } catch (Exception e) {
 796                         System.err.println("Exception Whilst trying to execute file " + sfile + " as a groovy script.");
 797                         e.printStackTrace(System.err);
 798
 799                 }
 800         }
 801
 802         public static boolean isHeadlessMode() {
 803                 String isheadless = System.getProperty("java.awt.headless");
 804                 if (isheadless != null && isheadless.equalsIgnoreCase("true")) {
 805                         return true;
 806                 }
 807                 return false;
 808         }
 809
 810         public AlignFrame[] getAlignFrames() {
 811                 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } : Desktop.getAlignFrames();
 812
 813         }
 814
 815         /**
 816          * Quit method delegates to Desktop.quit - unless running in headless mode when
 817          * it just ends the JVM
 818          */
 819         public void quit() {
 820                 if (desktop != null) {
 821                         desktop.quit();
 822                 } else {
 823                         System.exit(0);
 824                 }
 825         }
 826
 827         public static AlignFrame getCurrentAlignFrame() {
 828                 return Jalview.currentAlignFrame;
 829         }
 830
 831         public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) {
 832                 Jalview.currentAlignFrame = currentAlignFrame;
 833         }
 834 }